Public Member Functions | Static Public Member Functions | Static Public Attributes
EMAN::AutoMask2DProcessor Class Reference

Attempts to automatically mask out the particle, excluding other particles in the box, etc. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMask2DProcessor:
Inheritance graph
Collaboration diagram for EMAN::AutoMask2DProcessor:
Collaboration graph

List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
virtual string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "mask.auto2d"

Detailed Description

Attempts to automatically mask out the particle, excluding other particles in the box, etc.

thresholdruns from ~ -2 to 2, negative numbers for dark protein and positive numbers for light protein (stain).
filteris expressed as a fraction of the fourier radius.

Definition at line 5191 of file processor.h.

Member Function Documentation

virtual string EMAN::AutoMask2DProcessor::get_desc ( ) const [inline, virtual]

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

The description of this processor.

Implements EMAN::Processor.

Definition at line 5220 of file processor.h.

                        return "2D version of mask.auto3d";
virtual string EMAN::AutoMask2DProcessor::get_name ( ) const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

The processor's name.

Implements EMAN::Processor.

Definition at line 5196 of file processor.h.

References NAME.

                        return NAME;
virtual TypeDict EMAN::AutoMask2DProcessor::get_param_types ( ) const [inline, virtual]

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 5206 of file processor.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

                        TypeDict d;
                        d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. ");
                        d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses.");
                        d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass.");
                        d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma");
                        d.put("nshells", EMObject::INT, "The number of dilation operations");
                        d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations");
                        d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume.");
                        d.put("verbose", EMObject::INT, "How verbose to be (stdout)");
                        return d;
static Processor* EMAN::AutoMask2DProcessor::NEW ( ) [inline, static]

Definition at line 5201 of file processor.h.

                        return new AutoMask2DProcessor();
void AutoMask2DProcessor::process_inplace ( EMData image) [virtual]

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

imageThe image to be processed.

Implements EMAN::Processor.

Definition at line 5602 of file processor.cpp.

References abs, EMAN::EMData::calc_n_highest_locations(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_size(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::Dict::has_key(), ImageDimensionException, LOGWARN, EMAN::EMData::mult(), nx, EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::set_value_at(), and EMAN::EMData::update().

        if (!image) {
                LOGWARN("NULL Image");

        if (image->get_ndim() != 2) {
                throw ImageDimensionException("This processor only supports 2D images.");

         The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor
         To get around this just use the return_mask parameter.
        string mask_output = params.set_default("write_mask", "");
        if ( mask_output != "") {
                if (Util::is_file_exist(mask_output) ) throw InvalidParameterException("The mask output file name already exists. Please remove it if you don't need it.");
                if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized");

        int radius=0;
        if (params.has_key("radius")) {
                radius = params["radius"];
        int nmaxseed=0;
        if (params.has_key("nmaxseed")) {
                nmaxseed = params["nmaxseed"];

        float threshold=0.0;
        if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"];
        else threshold=params["threshold"];

        int nshells = params["nshells"];
        int nshellsgauss = params["nshellsgauss"];
        int verbose=params.set_default("verbose",0);

        int nx = image->get_xsize();
        int ny = image->get_ysize();

        EMData *amask = new EMData();
        amask->set_size(nx, ny);

        float *dat = image->get_data();
        float *dat2 = amask->get_data();
        int i,j;
        size_t l = 0;

        if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold);

        // Seeds with the highest valued pixels
        if (nmaxseed>0) {
                vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed);

                for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) {
                        if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value);

        // Seeds with a circle
        if (radius>0) {
                // start with an initial circle
                for (j = -ny / 2; j < ny / 2; ++j) {
                        for (i = -nx / 2; i < nx / 2; ++i,++l) {
                                if ( abs(j) > radius || abs(i) > radius) continue;
//                              if ( (j * j + i * i) > (radius*radius) || dat[l] < threshold) continue;         // torn on the whole threshold issue here. Removing it prevents images from being totally masked out
                                if ( (j * j + i * i) > (radius*radius) ) continue;
                                dat2[l] = 1.0f;

        // iteratively 'flood fills' the map... recursion would be better
        int done=0;
        int iter=0;
        while (!done) {
                if (verbose && iter%10==0) printf("%d iterations\n",iter);
                for (j=1; j<ny-1; ++j) {
                        for (i=1; i<nx-1; ++i) {
                                if (dat2[l]) continue;
                                if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) {


        if (verbose) printf("extending mask\n");
        amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss));

        bool return_mask = params.set_default("return_mask",false);
        if (return_mask) {
                // Yes there is probably a much more efficient way of getting the mask itself, but I am only providing a stop gap at the moment.
        } else {

        // EMAN2 policy is not to allow file io from with a processor
        //if (mask_output != "") {
        //      amask->write_image(mask_output);

        delete amask;

Member Data Documentation

const string AutoMask2DProcessor::NAME = "mask.auto2d" [static]

Definition at line 5225 of file processor.h.

Referenced by get_name().

The documentation for this class was generated from the following files: